Lessons learned from adapting the Darwin Core vocabulary standard for use in RDF

Abstract

The Darwin Core vocabulary is widely used to transmit biodiversity data in the form of simple text files. In order to support expression of biodiversity data in the Resource Description Framework (RDF), a guide was created as a non-normative addition to the Darwin Core standard. This paper describes the major issues that were addressed in the creation of the guide, particularly problems related to adapting terms designed to have literal values for use with IRI references. By making it possible to express millions of existing records as RDF, the guide is an important step towards enabling the biodiversity informatics community to participate in broader Linked Data and Semantic Web efforts.

Darwin-SW: Darwin Core-based terms for expressing biodiversity data as RDF

“…Expressing these data in the Resource Description Framework (RDF) 1 has a number of advantages over * Corresponding author simple fielded text formats (where a line in the file contains the data for a single record). Because of its graph-based syntax, 2 RDF supports the complex data structures required to merge diverse kinds of data about biodiversity resources. RDF's use of triples as the basic unit of information removes ambiguity about the resource with which a property is associated, a fundamental problem when data about several types of resources are combined in a single row of a database table.…”

“…12 Because of its widespread use, and since its terms are defined using RDF, there has been considerable interest in using the Darwin Core vocabulary to describe biodiversity resources in RDF. An RDF guide 13 for the Darwin Core standard provides guidelines for using Darwin Core property terms as RDF predicates [2]. However, because Darwin Core does not assume any particular data model, the RDF guide does not define object properties to link instances of its main classes (those classes that are not considered auxiliary terms).…”

Bioschemas & Schema.org: a Lightweight Semantic Layer for Life Sciences Websites

“…Towards this end, the schem a.org collaborative community defines vocabularies covering common entities and relationships (e.g., events, organizations, creative works) (Guha et al 2016). Websites can leverage these vocabularies to embed semantic annotations within web pages, in the form of markup using standard formats.…”

“…The Bioschemas community (Garcia et al 2017) aims to extend schema.org to support markup for Life Sciences websites. A major pillar lies in reusing types from schema.org as well as welladopted domain ontologies, while only proposing a limited set of new types.…”

“…We can think of additional profiles to account for biodiversity-related information. For instance, since taxonomic registers are the backbone of many web portals and databases, new profiles could describe taxa and scientific names while reusing welladopted vocabularies such as Darwin Core terms (Baskauf et al 2016) or TDWG ontologies (TDWG Vocabulary Management Task Group 2013). Fostering the use of such markup by web portals reporting traits, observations or museum collections could not only improve information discovery using search engines, but could also be a key to spur largescale biodiversity data integration scenarios.…”